Contacts of the strand formed by residues 261 - 268 (chain A) in PDB entry 4FYT
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 261 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A ARG* 4.9 3.4 + - - +
258A LEU* 3.2 26.5 + - + +
259A PRO 3.2 0.6 - - - -
260A GLU* 1.3 83.0 - - + +
262A PRO* 1.4 64.1 - - - +
263A ASN* 2.9 36.2 + - - +
264A TRP* 3.0 39.8 + - + +
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Residues in contact with PRO 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A LYS* 3.7 17.9 + - - +
257A PRO* 4.3 17.4 - - + +
258A LEU 3.4 11.4 - - - +
259A PRO 4.4 4.7 - - - +
260A GLU 4.4 2.0 - - - +
261A ASP* 1.4 84.2 - - - +
263A ASN* 1.3 58.4 + - - +
264A TRP 3.1 12.6 + - - +
265A ASN* 4.8 0.7 - - - +
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Residues in contact with ASN 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A PRO* 3.6 5.7 - - - +
241A LYS* 2.8 53.1 + - - +
242A ASP* 4.9 0.5 - - - +
261A ASP* 2.9 22.0 + - - +
262A PRO* 1.3 78.0 - - - +
264A TRP* 1.3 59.0 + - + +
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Residues in contact with TRP 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A ARG* 3.3 45.2 - - + +
91A PRO 3.4 27.8 - - - -
92A TYR* 3.8 26.5 - + - -
93A LEU 5.3 0.7 - - - -
238A ILE* 3.8 9.0 - - + -
239A HIS* 3.2 27.8 - - - -
240A PRO* 3.8 18.8 - - + -
257A PRO* 3.5 5.2 - - - +
258A LEU* 2.8 34.7 + - + -
261A ASP* 3.0 38.7 + - + +
262A PRO 3.8 3.1 - - - +
263A ASN* 1.3 87.8 - - + +
265A ASN* 1.3 64.2 + - - +
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Residues in contact with ASN 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A ILE* 3.3 7.1 - - - +
239A HIS* 2.7 54.2 + - + +
241A LYS* 3.4 18.4 + - - +
255A SER* 3.8 5.8 - - - -
256A THR 3.3 7.9 - - - +
257A PRO* 4.0 8.5 - - - +
262A PRO 4.8 1.0 - - - +
264A TRP* 1.3 76.5 - - - +
266A VAL* 1.3 63.7 + - - +
1004A NAG 1.4 67.4 + - - +
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Residues in contact with VAL 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A THR* 3.6 27.8 - - + -
237A LEU 3.7 3.1 - - - -
238A ILE* 4.2 11.0 - - + +
254A PRO 4.4 1.6 - - - +
255A SER* 3.4 5.2 - - - -
256A THR* 2.6 47.1 + - - +
257A PRO 4.5 0.9 - - - +
258A LEU* 3.8 35.7 - - + -
259A PRO* 5.0 2.7 - - + -
265A ASN* 1.3 75.7 - - - +
267A THR* 1.3 59.7 + - - +
268A GLU* 4.1 3.4 + - + +
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Residues in contact with THR 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A THR* 3.3 4.0 - - - -
237A LEU 2.8 39.2 + - - -
239A HIS* 2.7 27.5 + - - -
245A ALA* 4.0 11.7 + - + +
251A PRO* 4.2 15.9 - - + -
254A PRO 5.6 0.7 - - - -
255A SER* 2.4 32.5 + - - +
266A VAL* 1.3 69.6 - - - +
268A GLU* 1.3 65.9 + - - +
269A PHE* 3.7 29.7 - - + -
1004A NAG 4.4 0.3 + - - -
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Residues in contact with GLU 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A ASN* 5.3 8.2 - - - +
235A ILE 3.6 5.6 - - - +
236A THR* 3.6 22.2 + - + +
251A PRO* 3.3 7.6 - - - +
252A LYS* 2.7 64.0 + - + +
253A GLY 5.0 0.5 - - - +
254A PRO 5.6 2.2 + - - -
266A VAL* 4.1 4.6 + - + +
267A THR* 1.3 75.2 - - - +
269A PHE* 1.3 66.7 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il